Hi Thomas,
This is not possible in AMBER and even if it was I do not believe that it
will do what you actually think it will do. Any restraint to an image can
be recast as an internal restraint, since you have periodic boundaries and
cannot be anything other than this. Placing a minimum distance restraint
between the C terminal of your protein and the N terminal of an image is
exactly the same as placing the same restraint between the two ends of the
central protein with the distance and sign of the force constant just
adjusted for the imaging. In effect all you will actually do is squash the
two ends of your protein together compacting it which is what you
definitely don't want to do. Ultimately you need to make the size of your
solute box larger to avoid such periodic artifacts.
All the best
Ross
On 1/27/13 10:22 AM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
>Dear AMBER users,
>
>I would like to know if distance restraints between the protein in the
>primary cell and one of its periodic images are allowed. The C-terminal
>loop of my protein interacts at some point of the simulation with the
>N-terminus of the protein in a periodic cell, and stays there for a long
>time. To avoid that I would like to apply a force that moves away the
>C-terminal loop whenever it reaching a cutoff distance from the periodic
>image. Is this possible in AMBER?
>
>
>thanks,
>Thomas
>
>
>--
>
>======================================================================
>
>Thomas Evangelidis
>
>PhD student
>University of Athens
>Faculty of Pharmacy
>Department of Pharmaceutical Chemistry
>Panepistimioupoli-Zografou
>157 71 Athens
>GREECE
>
>email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
>website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sun Jan 27 2013 - 17:30:03 PST
